We have shown that electron energy loss spectroscopic imaging (EELS) in the scanning transmission electron microscope (STEM) can provide near single atom sensitivity for elements such as calcium, phosphorus and iron bound to proteins adsorbed onto thin carbon films. A spectrum-imaging system incorporating a 100x1340 pixel CCD detector has enabled the parallel collection of EELS data at each image pixel. Advantages of this system are (i) the low noise level, which provides higher analytical sensitivity, (ii) the short read-out time of around 10 ms, which enables faster acquisition, (iii) the two-dimensional array of square pixels, which allows exact correction for channel gain variations, and (iv) the improved point-spread function of the optical coupling of the detector array to the scintillator. Compensation for specimen drift is achieved in real-time by cross-correlating annular dark-field images recorded at the end of each scan line. We have implemented new software to improve the accuracy of spectral analysis to reduce the elemental detection limits further.